June 11, 2019

Definitions

Outbreak

According to the CDC, Epidemic refers to an increase, often sudden, in the number of cases of a disease above what is normally expected in that population in that area. Outbreak carries the same definition of epidemic, but is often used for a more limited geographic area.

Measles (Rubeola)

Measles is an acute viral illness caused by a virus in the family paramyxovirus, genus Morbillivirus. Measles is characterized by a prodrome of fever (as high as 105°F) and malaise, cough, coryza, and conjunctivitis, followed by a maculopapular rash. The rash spreads from head to trunk to lower extremities. Measles is usually a mild or moderately severe illness. However, measles can result in complications such as pneumonia, encephalitis, and death.

Methodology

  1. Measles data from January 1st, 2010 to May 30, 2019 was extracted from the CDC's webpage.

  2. R code was developed to load, summarize and plot the case data.

  3. Conclusions were derived from definitions, summary statistics and graphs.

  4. R Markdown and Plotly were used to create the final presentation.

R Code - Part 1

library(plotly)
library(dplyr)
library(formattable)

# Load data
measles <- read.csv("MeaslesCases_5_30_2019.csv")
head(measles, 3)
  Year Cases Months
1 2010    63     12
2 2011   220     12
3 2012    55     12
# Calc summary statistics 
measles$Rate <- measles$Cases / measles$Months
casesMedian <- median(measles$Cases)
rateMedian <- median(measles$Rate)

graphTitle <- paste0("Measles Reported Cases<br>",
                     "<span style=\"font-size: 85%;",
                     "color: #144e75\">",
                     "Jan 1st, 2010 to May 30, 2019</span>")

R Code - Part 2

# Create bar graph
p <- plot_ly(data = measles,
             x = ~Year,
             y = ~Cases,
             type = 'bar',
             name = 'Year Cases') %>%
    add_trace(y = ~Rate,
              name = 'Monthly Rate') %>%
    add_lines(y = casesMedian,
              x = ~c(min(Year)-.5, Year, max(Year)+.5),
              line = list(color = '#144E75',
                          dash = 'dash',
                          width = 2),
              name = "Case Median") %>% 
    add_lines(y = rateMedian,
              x = ~c(min(Year)-.5, Year, max(Year)+.5),
              line = list(color = '#144E75',
                          dash = 'dot',
                          width = 2),
              name = "Rate Median") %>% 
    layout(title = list(text = graphTitle,
           font = list(size=20)),
           margin = list(l = 10, r = 10, b = 50, t = 120, pad = 4),
           yaxis = list(title = 'Case Count'),
           xaxis = list(tickangle = 40),
           barmode = 'group')

US Measles Incidence 2010 - 2019


* Data extracted from the CDC Website.

** Use zoom and pan controls to view details.

*Data extracted from the CDC Website.

**Use zoom function to view details.

Conclusions

  • The total cases reported for the period between January 1st, 2010 and May 30, 2019 have a median of 187.5 cases per year.

  • The total cases reported from January 1st to May 30, 2019 were 981, that represents a 5.23 fold the median cases per year.

  • The median of the monthly cases rate for the last 10 years was 15.62 cases per month.

  • The monthly rate of cases reported from January 1st to May 30, 2019 was 196.2 cases per month, that represents a 12.56 fold the median cases per month for the 10 year period.

  • The data shows a significant increase from the normally reported cases for the first five months of 2019, that increase can be categorize as an outbreak by CDC's definition.


Thanks.